Index

A

add_hydrogen_CSO() (in module qp.protonate.fix)

add_oxo_sin() (in module qp.structure.convert_nhie_oxo) adjust_activesites() (in module qp.protonate.fix)

B

box_outlier_thres() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) build_heavy() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad)

build_hydrogen() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) build_model() (in module qp.structure.missing)

C

calc_dipole() (in module qp.analyze.multiwfn) calc_dist() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) calculate_centroid() (in module qp.manager.charge_embedding) calculate_dihedral() (in module qp.structure.convert_nhie_oxo) cap_chains() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) center_molden() (in module qp.analyze.molden) CenterResidue (class in qp.cluster.spheres) charge_scheme() (in module qp.analyze.multiwfn) check_all_jobs() (in module qp.analyze.checkup) check_atom_valence() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) check_charge() (in module qp.cluster.charge_count) check_disulfide() (in module qp.cluster.spheres) check_failure_mode() (in module qp.analyze.checkup) check_NC() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) check_submit_record() (in module qp.analyze.checkup)

classify_job() (in module qp.analyze.checkup) clean_occupancy() (in module qp.protonate.fix) clean_termini() (in module qp.structure.missing) combine_pdbs() (in module qp.cluster.struct_to_file) (in module qp.structure.combine_pdbs) complete_oligomer() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) compress_sequence() (in module qp.manager.create) compute_charge() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) (in module qp.protonate.ligand_prop) compute_spin() (in module qp.protonate.ligand_prop) convert_akg_to_sin() (in module qp.structure.convert_nhie_oxo) correct_ecp_charges_inplace() (in module qp.analyze.molden) count_electron() (in module qp.cluster.charge_count) count_residues() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) create_jobs() (in module qp.manager.create) create_marker() (in module qp.manager.submit)

D

define_residues() (in module qp.structure.missing)

delete_clashes() (in module qp.structure.missing) download() (in module qp.protonate.get_protoss)

E

extract_author() (in module qp.analyze.checkup)

extract_clusters() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad)

F

fetch_pdb() (in module qp.structure.setup) fill_dummy() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) find_and_convert_ligands_to_oxo() (in module qp.structure.convert_nhie_oxo) find_heavy() (in module qp.manager.create) find_histidines() (in module qp.structure.convert_nhie_oxo)

fix_numbering() (in module qp.structure.missing) fix_OXT() (in module qp.protonate.fix) flip_coordinated_HIS() (in module qp.protonate.fix) format_element() (in module qp.cluster.struct_to_file) format_plot() (in module qp.analyze.checkup) (in module qp.cluster.spheres)

G

get_atmrad_path() (in module qp.analyze.multiwfn) get_atom_range() (in module qp.analyze.multiwfn) get_center_residues() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) get_centers() (in module qp.structure.setup) get_chain_order() (in module qp.structure.missing) get_charge() (in module qp.manager.create) get_charges() (in module qp.manager.charge_embedding) get_coc() (in module qp.analyze.multiwfn) get_com() (in module qp.analyze.multiwfn) get_cpu_count() (in module qp.analyze.multiwfn) get_electronic() (in module qp.manager.create)

get_ff14SB_dict() (in module qp.manager.ff14SB_dict) get_grid() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) get_grid_coord_idx() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) get_next_neighbors() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) get_normalized_vector() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) get_pdbs() (in module qp.structure.setup) get_residues() (in module qp.structure.missing) get_settings_ini_path() (in module qp.analyze.multiwfn)

I

is_valid_dipole_file() (in module qp.analyze.multiwfn)

iterate_qm_output() (in module qp.analyze.multiwfn)

L

ligand_in_spheres() (in module qp.manager.create)

load_custom_charges() (in module qp.manager.charge_embedding)

M

make_res_key() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) manage_jobs() (in module qp.manager.submit) merge_centers() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) module qp.analyze qp.analyze.checkup qp.analyze.molden qp.analyze.multiwfn qp.cli qp.cluster qp.cluster.charge_count qp.cluster.spheres qp.cluster.spheres_bad qp.cluster.struct_to_file qp.manager qp.manager.charge_embedding qp.manager.create qp.manager.ff14SB_dict qp.manager.job_scripts qp.manager.submit qp.protonate qp.protonate.fix qp.protonate.get_protoss qp.protonate.ligand_prop qp.protonate.parse_output qp.structure qp.structure.combine_pdbs qp.structure.convert_nhie_oxo qp.structure.missing qp.structure.setup

P

parse_input() (in module qp.structure.setup) parse_log() (in module qp.protonate.parse_output) parse_pdb() (in module qp.manager.charge_embedding) parse_pdb_to_xyz() (in module qp.manager.charge_embedding) partial_res_info() (in module qp.protonate.fix) place_oxo_manually() (in module qp.structure.convert_nhie_oxo) plot_authors() (in module qp.analyze.checkup) plot_failure_modes_from_csv() (in module qp.analyze.checkup)

plot_failures() (in module qp.analyze.checkup) plot_voronoi_2d() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) plot_voronoi_3d() (in module qp.cluster.spheres_bad) prepare_jobs() (in module qp.manager.submit) process_molden() (in module qp.analyze.molden) prune_atoms() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad)

Q

qp.analyze module qp.analyze.checkup module qp.analyze.molden module qp.analyze.multiwfn module qp.cli module qp.cluster module qp.cluster.charge_count module qp.cluster.spheres module qp.cluster.spheres_bad module qp.cluster.struct_to_file module qp.manager module qp.manager.charge_embedding module qp.manager.create module

qp.manager.ff14SB_dict module qp.manager.job_scripts module qp.manager.submit module qp.protonate module qp.protonate.fix module qp.protonate.get_protoss module qp.protonate.ligand_prop module qp.protonate.parse_output module qp.structure module qp.structure.combine_pdbs module qp.structure.convert_nhie_oxo module qp.structure.missing module qp.structure.setup module

R

read_config() (in module qp.structure.setup) read_pdb() (in module qp.manager.charge_embedding) (in module qp.structure.convert_nhie_oxo) read_xyz() (in module qp.manager.charge_embedding) record_type() (in module qp.protonate.parse_output) remove_atoms_from_pdb() (in module qp.manager.charge_embedding) remove_oxo_hydrogens() (in module qp.structure.convert_nhie_oxo)

remove_qm_atoms() (in module qp.manager.charge_embedding) rename_and_clean_resnames() (in module qp.manager.charge_embedding) repair_ligands() (in module qp.protonate.get_protoss) res_priority() (in module qp.protonate.fix) residue_exists() (in module qp.manager.create) residue_in_ligands() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad)

S

scale_hydrogen() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad)

submit() (in module qp.protonate.get_protoss) submit_jobs() (in module qp.manager.submit)

T

to_xyz() (in module qp.cluster.struct_to_file)

transfer_numbering() (in module qp.structure.missing) translate_to_origin() (in module qp.analyze.molden)

U

update_oxo_sdf() (in module qp.structure.convert_nhie_oxo)

update_sin_sdf() (in module qp.structure.convert_nhie_oxo) upload() (in module qp.protonate.get_protoss)

V

visualize_dummy() (in module qp.cluster.spheres)

voronoi() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad)

W

welcome() (in module qp.cli) write_alignment() (in module qp.structure.missing) write_author_credit_csv() (in module qp.analyze.checkup) write_pdb() (in module qp.manager.charge_embedding) (in module qp.structure.convert_nhie_oxo)

write_pdbs() (in module qp.cluster.spheres) (in module qp.cluster.spheres_bad) write_qm() (in module qp.manager.job_scripts) write_sge_job() (in module qp.manager.job_scripts) write_slurm_job() (in module qp.manager.job_scripts)